There is a strong interest in the detection of microorganisms such as bacteria and other microorganisms in both biological and food based samples. Bacterial pathogens can cause substantial morbidity among humans and domestic animals, as well as immense economic loss. Also, detection of microorganisms is a high priority within the Food and Drug Administration (FDA) given outbreaks of life-threatening or fatal illness caused by ingestion of food contaminated with certain microorganisms e.g., Escherichia coli or Salmonella spp.
Traditional microbiological tests for the detection of bacteria and viruses rely on non-selective and selective enrichment cultures followed by plating on selective media and further testing to confirm suspect colonies. Such procedures can require several days. A variety of rapid methods have been investigated and introduced into practice to reduce the time requirement. However, these methods have drawbacks. For example, techniques involving immunoassays or gene probes generally require an enrichment step in order to obtain adequate sensitivity. Polymerase chain reaction (PCR) tests also include an amplification step and therefore are capable of both very high sensitivity and selectivity. However, the sample size that can be economically subjected to PCR testing is limited. With dilute bacterial suspensions, most small subsamples will be free of cells and therefore enrichment steps are still required. The time required for biological enrichment is dictated by the growth rate of the target bacterial population of the sample, by the effect of the sample matrix, and by the required sensitivity. For instance, a magnetic-capture PCR system for verotoxigenic E. coli can require about 5, 7, and 10 hours enrichment to detect 1000, 100, and 1 colony forming unit per milliliter (cfu/ml), respectively, in a model system, and 15 hours enrichment to detect 1 cfu per gram (g) in ground beef. In practice, most high sensitivity methods employ an overnight incubation and take about 24 hours overall. Due to the time required for cultivation, these methods can take up to three days, depending upon the organism to be identified and the source of the sample. This lag time is generally unsuitable as the contaminated food, water (or other product) may have made its way into livestock or humans. In addition, increases in antibiotic-resistant bacteria and biodefense considerations make rapid identification of bacterial pathogens in water, food, and clinical samples critical priorities worldwide.
Also, there is a strong interest in the detection of the levels of metabolites and other biomolecules. Such biomolecules may be derived from microorganisms of interest. Assays for protein biomolecules may utilize antibodies that recognize the protein of interest. Or, assays for detection of peptides or non-protein biomolecules may involve partial purification and chemical analysis using systems such as chromatography and mass spectrometry. Or, nucleic acid probes may be used to detect levels of mRNA in a sample.
Generally, however, such methods may take up to several days and/or require a significant amount of a material. For example, techniques involving immunoassays or gene probes generally require an enrichment step in order to obtain adequate sensitivity. Polymerase chain reaction (PCR) tests include an amplification step to obtain very high sensitivity and selectivity. Also, the sample size that can be economically subjected to PCR testing is limited.
Therefore, there is a need for more rapid, simple, and sensitive detection and identification of microorganisms, such as bacteria and other potentially pathogenic microorganisms. There is also a need for direct, rapid, simple, and sensitive detection and identification of biomolecules that may be of clinical relevance.